Variant report

Variant	rs17073107
Chromosome Location	chr6:144166216-144166217
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143827995..143830222-chr6:144165832..144168637,2	K562	blood:
2	chr6:144127689..144129702-chr6:144164044..144166311,2	K562	blood:

Variant related genes	Relation type
ENSG00000257065	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11155329	0.84[AFR][1000 genomes]
rs17073138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073142	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896679	0.86[AFR][1000 genomes]
rs4896684	0.83[GIH][hapmap]
rs6932564	0.80[EUR][1000 genomes]
rs7454959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1034894	chr6:144148566-144170036	Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17073107	LTV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144165200-144166400	Weak transcription	Colonic Mucosa	Colon
2	chr6:144165200-144169800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:144165400-144166400	Weak transcription	Aorta	Aorta
4	chr6:144165400-144166400	Weak transcription	Spleen	Spleen
5	chr6:144165400-144166600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:144165400-144166600	Weak transcription	Gastric	stomach
7	chr6:144165400-144166800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:144165400-144168200	Weak transcription	Esophagus	oesophagus
9	chr6:144165400-144168400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:144165400-144172800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:144165400-144178400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:144165600-144166400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:144165600-144166400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:144165600-144166400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:144165600-144166400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:144165600-144166400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:144165600-144166400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
18	chr6:144165600-144166400	Genic enhancers	HUVEC	blood vessel
19	chr6:144165600-144166600	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:144165600-144166800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:144165600-144166800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr6:144165600-144167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:144165600-144169000	Weak transcription	Right Ventricle	heart
24	chr6:144165600-144172200	Weak transcription	Right Atrium	heart
25	chr6:144165600-144172600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:144165600-144172600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:144165600-144173600	Strong transcription	Placenta	Placenta
28	chr6:144165600-144175800	Weak transcription	Fetal Heart	heart
29	chr6:144165600-144175800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:144165600-144178400	Weak transcription	Stomach Mucosa	stomach
31	chr6:144165600-144186800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:144165800-144166400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:144165800-144166400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:144165800-144166400	Genic enhancers	Liver	Liver
35	chr6:144165800-144166400	Weak transcription	Brain Angular Gyrus	brain
36	chr6:144165800-144166400	Weak transcription	Fetal Intestine Small	intestine
37	chr6:144165800-144166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:144165800-144166800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:144165800-144166800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr6:144165800-144167000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:144165800-144167000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:144165800-144167400	Genic enhancers	HepG2	liver
43	chr6:144165800-144169600	Weak transcription	Small Intestine	intestine
44	chr6:144165800-144172000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:144165800-144172200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:144165800-144172200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:144165800-144172600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:144165800-144172600	Strong transcription	Fetal Stomach	stomach
49	chr6:144165800-144172800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:144165800-144172800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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